Abstract 4213: Multiplex digital spatial profiling of proteins and RNA in MC38 mouse colorectal cancer syngeneic model

Abstract

Abstract Introduction Characterization of the tumor microenvironment (TME) has become an essential step for the understanding of the complexity of cell interactions and the discovery of biomarkers for prediction and prognosis of immunotherapy response1. The NanoString GeoMx® Digital Spatial Profiler (DSP) technology includes the ability to quantitatively assess RNA and protein levels as well as sample multiple user-defined regions of interest, specifically focused on defining heterogeneity and TME interactions2. This technology has been widely used to identify biomarkers in clinical surgical specimens, but its applications in preclinical models are still needed. MC38 colorectal cancer syngeneic model is one of the most utilized models for assessing anti-cancer immunotherapies. In this study, we present the spatial profiling of proteins and RNA on MC38 model treated with anti-PD-1 through GeoMx® DSP technology. Methods GeoMx protein panel was used to detect the target protein expression differential in tumor-rich region and immune-rich region within MC38 subcutaneous tumor sections treated. Mice were treated with vehicle or anti-PD-1 (10mg/kg, BIW x 4 doses, ip). Whole Transcriptome Atlas (WTA) was employed, and then a comprehensive assessment of the data and comparison was performed. Results Two morphology markers, CD45 and PanCK, were used to separate tumor-rich region and immune-rich region. The GeoMx® protein data showed that the abundance of VISTA in tumor-rich region differed significantly (log2(fold-change) = 0.67, p < 0.01) in anti-PD-1 group compared to vehicle group. While in immuno-rich region, GITR was significantly altered (log2(fold-change) = 0.79, p < 0.05) in anti-PD-1 group (TGI value = 50.39%). From WTA data, we observed the upregulation of 839 genes, while 1048 genes were downregulated in immuno-rich region in anti-PD-1 group compared with vehicle group (p < 0.05). For tumor-rich regions, 550 genes were upregulated while 782 genes were downregulated in anti-PD-1 group versus vehicle group (p < 0.05). From the gene set enrichment analysis, we found that interferon alpha and interferon gamma, which are related to tumor immunity and immunotherapy response, were upregulated in anti-PD-1 group. Conclusion Both the differential expressing genes and proteins in TME of MC38 syngeneic models treated with anti-PD-1 could be well detected by GeoMx® DSP, which has the potential to provide insightful data for use in biomarker discovery in preclinical cancer models. References Charmsaz S, Collins DM, Perry AS, Prencipe M. Novel Strategies for Cancer Treatment: Highlights From the 55th IACR Annual Conference. Cancers (Basel) 2019; 11(8). Toki MI, et al. High-plex predictive marker discovery for melanoma immunotherapy-treated patients using digital spatial profiling. Clin. Cancer Res. 2019;25:5503-5512. Citation Format: Meihui Chen, Hengyuan Liu, Xiaolong Tu, Sheng Guo, Xiaobo Chen. Multiplex digital spatial profiling of proteins and RNA in MC38 mouse colorectal cancer syngeneic model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4213.